I'm in the uk where Amelia, Matilda, Henry, Theo & Benjamin are all very popular at the moment whereas Ezra is almost unheard of. I'm not sure whether this should influence my decision. Middle names are just ideas, not set in stone.
Which do you like best with Ezra? Any other suggestions?

I like Hattie best from your girl list. Ezra and Hattie.
I agree with niteowl about AsherGabriel from your boy list. Ezra and Asher.
My second favorite is Jonah. Ezra and Jonah.
I think since Ezra is not popular in the UK, you should choose one of the less popular names from your list as well.